Update and polish pipestat docs

README.md

@@ -41,7 +41,7 @@ The documentation is published automatically upon commits to `master` using a Gi
 In the past, I had a plugin that would auto-document 2 things: 1. Python docs using lucidoc, and 2. Jupyter notebooks. This plugin was neat, but it caused me a lot of maintenance issues as well. So now, I've made it much simpler; now it's no longer a plugin, just a simple Python script. Update all the auto-generated docs (stored in `docs/autodoc_build`) by running the update script manually:
 
 ```console
-python update_python_autodocs.py
+python autodoc.py
 ```
 
 #### Configuring lucidoc rendering

docs/eido/code/cli.md

@@ -80,7 +80,7 @@ eido validate peppro_paper.yaml -s http://schema.databio.org/pep/2.0.0.yaml -e
     Validation successful
 
 
-Any PEP should validate against that schema, which describes generic PEP format. We can go one step further and validate it against the PEPPRO schema, which describes Proseq projects specifically for this pipeline:
+Any PEP should validate against that schema, which describes generic PEP format. We can go one step further and validate it against the PEPPRO schema, which describes Proseq projects specfically for this pipeline:
 
 
 ```bash
@@ -144,7 +144,7 @@ eido validate -h
 
 Let's use `eido convert` command to convert PEPs to a variety of different formats. `eido` supports a plugin system, which can be used by other tool developers to create Python plugin functions that save PEPs in a desired format. Please refer to the documentation for more details. For now let's focus on a couple of plugins that are built-in in `eido`.
 
-To see what plugins are currently available in your Python environment call:
+To see what plugins are currently avaialable in your Python environment call:
 
 
 ```bash
@@ -213,6 +213,8 @@ eido convert peppro_paper.yaml --format csv
     H9_treated_PRO-seq_1,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_200nM_romidepsin_rep1_PE1.fastq.gz,PAIRED,H9 treated PRO-seq,H9_treated_PRO-seq_1,H9_200nM_romidepsin_rep1,200 nM romidepsin,8,/Users/mstolarczyk/H9_200nM_romidepsin_rep1_PE2.fastq.gz
     H9_treated_PRO-seq_2,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_200nM_romidepsin_rep2_PE1.fastq.gz,PAIRED,H9 treated PRO-seq,H9_treated_PRO-seq_2,H9_200nM_romidepsin_rep2,200 nM romidepsin,8,/Users/mstolarczyk/H9_200nM_romidepsin_rep2_PE2.fastq.gz
     H9_treated_PRO-seq_3,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_200nM_romidepsin_rep3_PE1.fastq.gz,PAIRED,H9 treated PRO-seq,H9_treated_PRO-seq_3,H9_200nM_romidepsin_rep3,200 nM romidepsin,8,/Users/mstolarczyk/H9_200nM_romidepsin_rep3_PE2.fastq.gz
+
+
     H9_PRO-seq_10,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_PRO-seq_10pct_PE1.fastq.gz,PAIRED,10% subset H9 PRO-seq 2,H9_PRO-seq_10,H9_PRO-seq_10pct,DMSO,8,/Users/mstolarczyk/H9_PRO-seq_10pct_PE2.fastq.gz
     H9_PRO-seq_20,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_PRO-seq_20pct_PE1.fastq.gz,PAIRED,20% subset H9 PRO-seq 2,H9_PRO-seq_20,H9_PRO-seq_20pct,DMSO,8,/Users/mstolarczyk/H9_PRO-seq_20pct_PE2.fastq.gz
     H9_PRO-seq_30,hg38,human,['$CODE/peppro/sample_pipeline_interface.yaml'],human_rDNA,PRO,/Users/mstolarczyk/H9_PRO-seq_30pct_PE1.fastq.gz,PAIRED,30% subset H9 PRO-seq 2,H9_PRO-seq_30,H9_PRO-seq_30pct,DMSO,8,/Users/mstolarczyk/H9_PRO-seq_30pct_PE2.fastq.gz

docs/eido/code/demo.md

@@ -129,7 +129,7 @@ required:
   - samples
 ```
 
-PEPs to successfully validate against this schema will need to fulfill all the generic PEP2.0.0 schema requirements _and_ fulfill the new `my_numeric_attribute` requirement.
+PEPs to succesfully validate against this schema will need to fulfill all the generic PEP2.0.0 schema requirements _and_ fulfill the new `my_numeric_attribute` requirement.
 
 ### How importing works
 
@@ -306,7 +306,7 @@ validate_project(project=p, schema="../tests/data/schemas/test_schema_invalid.ya
 
 ## Config validation
 
-Similarly, the config part of the PEP can be validated; the function inputs remain the same
+Similarily, the config part of the PEP can be validated; the function inputs remain the same
 
 
 ```python
@@ -326,7 +326,7 @@ validate_sample(
 
 ## Output details
 
-As depicted above the error raised by the `jsonschema` package is very detailed. That's because the entire validated PEP is printed out for the user reference. Since it can get overwhelming in case of the multi sample PEPs each of the `eido` functions presented above provide a way to limit the output to just the general information indicating the unmet schema requirements
+As depicted above the error raised by the `jsonschema` package is very detailed. That's because the entire validated PEP is printed out for the user reference. Since it can get overwhelming in case of the multi sample PEPs each of the `eido` functions presented above privide a way to limit the output to just the general information indicating the unmet schema requirements
 
 
 ```python

docs/geofetch/changelog.md

@@ -1,5 +1,20 @@
 # Changelog
 
+## [0.12.8] -- 2025-07-08
+- Updated docs
+- Fixed parsing nested items. [[143](https://github.com/pepkit/geofetch/issues/143)]
+- Added pypiper to requirements [[142](https://github.com/pepkit/geofetch/issues/142)]
+- Fixed white spaces in reference genome string [[141](https://github.com/pepkit/geofetch/issues/141)]
+- Added version in CLI help [[135](https://github.com/pepkit/geofetch/issues/135)]
+- Updated SRA convert to use looper > 2.0.0 and fully automate process
+
+## [0.12.7] -- 2024-09-11
+- Updated Python support 3.13
+- Cleaned code and Readme
+
+## [0.12.6] -- 2024-02-05
+- Updated support for Windows in Prefetch (Note: Some functionality may still be unavailable on Windows)
+
 ## [0.12.5] -- 2023-11-29
 - Fixed bug, where description was not populated in PEP